Crystal structure, Hirshfeld surface analysis, inter-molecular inter-action energies, energy frameworks and DFT calculations of 4-amino-1-(prop-2-yn-1-yl)pyrimidin-2(1 H)-one

Mouad Lahyaoui; Amal Haoudi; Badr Eddine Kartah; Ahmed Mazzah; Tuncer Hökelek; Joel T Mague; Youssef Kandri Rodi; Nada Kheira Sebbar

doi:10.1107/S2056989023009933

Crystal structure, Hirshfeld surface analysis, inter-molecular inter-action energies, energy frameworks and DFT calculations of 4-amino-1-(prop-2-yn-1-yl)pyrimidin-2(1 H)-one

Acta Crystallogr E Crystallogr Commun. 2023 Nov 21;79(Pt 12):1183-1189. doi: 10.1107/S2056989023009933. eCollection 2023 Dec 1.

Authors

Mouad Lahyaoui¹, Amal Haoudi², Badr Eddine Kartah³, Ahmed Mazzah⁴, Tuncer Hökelek⁵, Joel T Mague⁶, Youssef Kandri Rodi⁷, Nada Kheira Sebbar^{8

3}

Affiliations

¹ Laboratoire de Chimie Organique Appliquée, Université Sidi Mohamed Ben Abdallah, Faculté des Sciences et Techniques, Route d'Immouzzer, BP 2202 Fez, Morocco.
² Laboratory Of Applied Organic Chemistry, Sidi Mohamed Ben Abdellah University, Faculty Of Science And Technology, Road Immouzer, BP 2202 Fez, Morocco.
³ Laboratory of Plant Chemistry, Organic and Bioorganic Synthesis, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, BP 1014 RP, Morocco.
⁴ Science and Technology of Lille USR 3290, Villeneuve d'ascq cedex, France.
⁵ Department of Physics, Hacettepe University, 06800 Beytepe, Ankara, Türkiye.
⁶ Department of Chemistry, Tulane University, New Orleans, LA 70118, USA.
⁷ Laboratoire de Chimie Organique Appliquée, Université Sidi Mohamed Ben Abdallah, Faculté des Sciences et Techniques, Route dImmouzzer, BP 2202 Fez, Morocco.
⁸ Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco.

Abstract

In the title mol-ecule, C₇H₇N₃O, the pyrimidine ring is essentially planar, with the propynyl group rotated out of this plane by 15.31 (4)°. In the crystal, a tri-periodic network is formed by N-H⋯O, N-H⋯N and C-H⋯O hydrogen-bonding and slipped π-π stacking inter-actions, leading to narrow channels extending parallel to the c axis. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (36.2%), H⋯C/C⋯H (20.9%), H⋯O/O⋯H (17.8%) and H⋯N/N⋯H (12.2%) inter-actions, showing that hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions. The mol-ecular structure optimized by density functional theory (DFT) calculations at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The HOMO-LUMO behaviour was also elucidated to determine the energy gap.

Keywords: amino group; crystal structure; heterocyclic compound; hydrogen bonding.

Grants and funding

JTM thanks Tulane University for support of the Tulane Crystallography Laboratory. TH is grateful to Hacettepe University Scientific Research Project Unit (grant No. 013 D04 602 004).